Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope.
Journal, issue, pages	Nat Microbiol, Vol. 7, Issue 10, Page 1635-1649, Year 2022
Publish date	Sep 23, 2022
Authors	Ping He / Banghui Liu / Xijie Gao / Qihong Yan / Rongjuan Pei / Jing Sun / Qiuluan Chen / Ruitian Hou / Zimu Li / Yanjun Zhang / Jincun Zhao / Hao Sun / Bo Feng / Qian Wang / Haisu Yi / Peiyu Hu / Pingchao Li / Yudi Zhang / Zhilong Chen / Xuefeng Niu / Xiaolin Zhong / Liang Jin / Xiaofeng Liu / Kun Qu / Katarzyna A Ciazynska / Andrew P Carter / John A G Briggs / Jizheng Chen / Jinsong Liu / Xinwen Chen / Jun He / Ling Chen / Xiaoli Xiong /
PubMed Abstract	Population antibody response is thought to be important in selection of virus variants. We report that SARS-CoV-2 infection elicits a population immune response that is mediated by a lineage of VH1- ...Population antibody response is thought to be important in selection of virus variants. We report that SARS-CoV-2 infection elicits a population immune response that is mediated by a lineage of VH1-69 germline antibodies. A representative antibody R1-32 from this lineage was isolated. By cryo-EM, we show that it targets a semi-cryptic epitope in the spike receptor-binding domain. Binding to this non-ACE2 competing epitope results in spike destruction, thereby inhibiting virus entry. On the basis of epitope location, neutralization mechanism and analysis of antibody binding to spike variants, we propose that recurrent substitutions at 452 and 490 are associated with immune evasion of the identified population antibody response. These substitutions, including L452R (present in the Delta variant), disrupt interactions mediated by the VH1-69-specific hydrophobic HCDR2 to impair antibody-antigen association, enabling variants to escape. The first Omicron variants were sensitive to antibody R1-32 but subvariants that harbour L452R quickly emerged and spread. Our results provide insights into how SARS-CoV-2 variants emerge and evade host immune responses.
External links	Nat Microbiol / PubMed:36151403 / PubMed Central
Methods	EM (single particle)
Resolution	3.73 - 6.75 Å
Structure data	33748 7ydi EMDB-33748: Spike_GSAS_6P protomer RBD domain bound with R1-32 Fab and ACE2 with 3:3:3 ratio PDB-7ydi: SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 3 ACE2, focused refinement of RBD region Method: EM (single particle) / Resolution: 3.98 Å 33760 7ydy EMDB-33760: Spike_GSAS_6P and R1-32 Fab with 3to1 ratio PDB-7ydy: SARS-CoV-2 Spike (6P) in complex with 1 R1-32 Fab Method: EM (single particle) / Resolution: 4.75 Å 33764 7ye5 EMDB-33764: SARS-COV-2 Spike_GSAS_6P bound with two R1-32 Fabs PDB-7ye5: SARS-CoV-2 Spike (6P) in complex with 2 R1-32 Fabs Method: EM (single particle) / Resolution: 6.75 Å 33766 7ye9 EMDB-33766, PDB-7ye9: SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs Method: EM (single particle) / Resolution: 4.17 Å 33772 7yeg EMDB-33772, PDB-7yeg: SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 3 ACE2 Method: EM (single particle) / Resolution: 3.73 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine
Source	homo sapiens (human) severe acute respiratory syndrome coronavirus 2
Keywords	VIRAL PROTEIN/IMMUNE SYSTEM / antibodies / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / ACE2